CardamomOT.tools.plot_results_sim
=================================

.. py:module:: CardamomOT.tools.plot_results_sim

.. autoapi-nested-parse::

   Plotting utilities for comparing data, mixture, trajectories, and simulations.



Functions
---------

.. autoapisummary::

   CardamomOT.tools.plot_results_sim.plot_results_rna_mixture
   CardamomOT.tools.plot_results_sim.plot_results_rna_clean
   CardamomOT.tools.plot_results_sim.plot_results_prot


Module Contents
---------------

.. py:function:: plot_results_rna_mixture(split, p, project_on_full=False, normtransform=False, logtransform=True)

   Compare observed data to the NB mixture fit (UMAP by time and cell type).

   :param split: Data split to load (``"full"`` or ``"train"``).
   :type split: str
   :param p: Path to the project directory (trailing slash included).
   :type p: str
   :param project_on_full: If True, fit UMAP on data and project mixture; otherwise fit jointly.
   :type project_on_full: bool
   :param normtransform: Apply total-count normalisation before UMAP.
   :type normtransform: bool
   :param logtransform: Apply log1p transformation before UMAP.
   :type logtransform: bool


.. py:function:: plot_results_rna_clean(p, stim=1.0, prior=1.0, project_on_full=False, normtransform=False, logtransform=True)

   Compare inferred RNA trajectories across all pipeline stages (UMAP).

   Loads reference (NB mixture), network modes, RNA trajectories, and
   simulated data, then plots time and cell-type UMAPs for all four.

   :param split: Data split (``"full"`` or ``"train"``).
   :type split: str
   :param p: Path to the project directory (trailing slash included).
   :type p: str
   :param stim: Stimulus-edge penalisation value used during inference.
   :type stim: float
   :param prior: Prior-network weighting value used during inference.
   :type prior: float
   :param project_on_full: If True, fit UMAP on the NB mixture and project others.
   :type project_on_full: bool
   :param normtransform: Apply total-count normalisation before UMAP.
   :type normtransform: bool
   :param logtransform: Apply log1p transformation before UMAP.
   :type logtransform: bool


.. py:function:: plot_results_prot(p, stim=1.0, prior=1.0, project_on_full=True)

   Compare protein trajectories and simulations (UMAP colored by time).

   :param p: Path to the project directory (trailing slash included).
   :type p: str
   :param stim: Stimulus-edge penalisation value used during inference.
   :type stim: float
   :param prior: Prior-network weighting value used during inference.
   :type prior: float
   :param project_on_full: If True, fit UMAP on trajectories and project simulations.
   :type project_on_full: bool